An Unexpected Journey
by SVUVOYFAN24
Summary: When Captain Janeway is faced with a surprise she never expected, she will have to go through this journey with a man she never knew she could be with. J/C!
1. Chapter 1

Just another morning on Voyager, Captain Janeway is waking up from her usual two hour slumber. She sleepily strides over to her replicator.

"Coffee, black." She yawns.

She hold onto the coffee like it's her life line. She takes two sips and sits it down on her desk. She then lays out her uniform on her bed.

"Another day in the delta quadrant. It better be a normal one!" She says aloud.

She begins to feel something coming up her throat. She runs over to the toilet and vomits, her throat burning as she heaved.

"What the hell! This is the fifth time this week!" She exclaims as she lay over the toilet, wiping off her mouth.

She turns on the sonic shower. She begins to let her night gown fall off her shoulders and down her body. She steps in and lets the soft pulses hit her aching back. She steps out of the shower and strides over to her bed. She puts on her uniform and grabs a PADD. It had Tuvok's weekly security report on it. She didn't get a chance to read it last night because she was too busy making friends with her toilet! She exits her quarters and starts to walk toward the turbo lift. She passes many crewmen on the way, nodding and smiling at her. She of course smiles back. She gets to the turbo lift. The doors swish behind her as she enters. She spins around facing the doors.

"Bridge!" she tells the turbo lift.

As it starts to move she starts to feel dizzy. She begins to get pounding headaches in her temples.

"Halt turbo lift!" she says.

She puts her free hand on her head, messaging her right temple. The pain began to fade.

"Resume turbo lift!" She says as she places her hand on the bridge of her nose.

She enters the bridge, crewman start to face her.

"Captain on the bridge!" Harry announces

"As you were!" She says back. She begins to walk to the captain's chair. "Lieutenant Paris, what is our present course?"

"Our present course is to the alpha quadrant." He replies.

She nodes. Chakotay is sitting next to her looking at his console. All Kathryn can do is picture him sitting there. Those perfect muscles flexing as he moved his arm. She began to read the extremely boring security report. She all of a sudden drops it on the floor. Then a sharp pain hits her in the temple. She grabs her head. Chakotay bends down to grab it.

"Captain are you alright?" He whispers.

"I'm fine. I just have a headache." she whispers back, feeling bad that she lied to him. She isn't fine.

"We need to talk." He whispers.

"Okay…" She whispers raising her right eyebrow.

She gets up and begins to walk towards her ready room. Tuvok was standing at tactical with his eyebrow raised as he watched Chakotay follow her.

The door swishes closed behind Chakotay.

"What is it Commander? " She asks as she plops herself onto her sofa.

"You tell me!" He says back.

"Excuse me?" She replies confused.

"You haven't been looking very well. For the past few days you have been late to your shift. That worries me!" He says.

"I've only been a few minutes late. Is that a crime?" She asks.

"Kathryn, you're never late. If anything, you're early!" He says.

She starts to stand up but goes right back down. Chakotay runs over to her.

"Are you sure you don't need to go to sickbay?" He asks.

"I'm fine, you worry too much!" She replies.

He places his hand on her thigh. "Kathryn, please…"

She looks down at his hand and pushes it off. He looks at her, stunned.

"Chakotay…" she whispers, "We can't, we set parameters"

"We kind of broke those parameters four months ago!" He says with a smirk.

She begins to remember that beautiful night, a night she will never forget. Then she remembers.

"That was a mistake!" She replies, shaking her head,

"No, it wasn't, at least not to me!" He says gently.

Kathryn looks down at her lap, thinking. Chakotay gently lifts her chin up with his fingers. Tears start to stream down her face. Chakotay wipes them off. She grabs his hands and holds them in her lap. She had never cried in front of him before, but it felt good to release.

She looks at him, directly in the eyes.

"Chakotay, we can't. It would be completely unprofessional for the captain and her first officer to be involved!" She cries.

"Kathryn, we are thousands of light years away from Starfleet! Who cares if we're together? B'Elanna and Tom are together and they're two senior officers." He argues.

"B'Elanna's not the captain and Tom's not the first officer." She replies, wiping away the tears on her face.

"But Kathryn…" he grabs her hands and holds them tightly. He stares into her deep blue eyes. "I love you."

Tears begin to escape from her eyes. "Chakotay…" She pauses, looking down at their entangled hands. "I love you too, but we just can't. What will the crew think of it?" She says as she looks back into his eyes.

His eyes begin to tear up. Looking in disbelief that she cares about what the crew thinks! She had never seen him cry before. She thought it was kind of cute the way the tears fell of his chin.

"There are thousands of rumors swarming around this ship about us being together." He admits.

She sat there thinking and then remembered. "I'm sorry, but we can't. We made an agreement on New Earth." She wipes her face.

She then wipes the tears falling down Chakotay's face. He holds her hand to his face looking into her eyes. She then gets up, his hand still holding hers. She begins to walk towards the doors, when she feels Chakotay still holding on to her hand. She pulls away, again walking towards the doors.

"Wait!" Chakotay says before she gets to the door.

She stops and spins around to look at him.

"At least go to sickbay and see what's wrong." He asks, while wiping the remaining tears on his face off.

"Fine!" She says as she walks out of the ready room.

Chakotay follows her. The crewmen on the bridge turn around to look at them. Chakotay walks to his chair and sits down, fondling with the console. Kathryn walks to the turbo lift. Chakotay's eyes are a puffy and red, Tom turns around to look at them. He then turns to Harry. Harry shrugs his shoulders and returns to his console at Ops. Tom looks back at the view screen with a confused look on his face. Wondering what happened in that ready room.

"Commander, you have the bridge." She says as she enters the turbo lift. "Deck five!"

She begins to feel dizzy again. She pinches the bridge of her nose. She become light headed, and everything goes black.

 **This is my first Fan Fiction, so bare with me! Please leave reviews and inferences on what you think will happen next! I'm open to requests!**


	2. Chapter 2

She opens her eyes and everything seems blurry.

"Captain, you're awake!" the Doctor says.

Her vision begins to clear up.

"Wh…What happened?" She asked, looking around realizing she was in sickbay.

"You fainted in the turbo lift, B'elanna found you!" He says as he scans her.

She sits up holding her head. "How long have I been out?" She asks.

"About an hour." He said, closing the tricorder.

"What! Why did I faint?" She asks concerned.

"Umm, captain have you been feeling dizzy and vomiting?" He asks, raising his right eyebrow.

"Yes, that's what I was coming to sickbay to see about." She says.

The doctor walks over to the medical console. He's looking at the captain's medical records, with a worried look on his face. Like he feels bad about what he's about to say.

"Captain…"He starts.

"What's wrong doctor!" She urges.

"Captain, you're… you're pregnant." He says, feeling guilty about the words that just came out. He was scared, scared for what her reaction might be.

She turns completely pale, "Wh… What!" She says. "How long?" She whispers.

"Four months." He replies. He's still scared; his holographic shoulders tense up, as he holds his artificial breath.

"Umm, thank you Doctor," She says as tears build up in her eyes. There's a long pause."I, uh, I need to go." She finally says. She gets up from the bio-bed and starts to slowly walk towards the door.

"Hold on, do you want it? I can termin…"

"No! I can't do that." She says. She exits sickbay scared as hell. Not knowing what to do for the first time in her life! She wishes her mother was there to talk her through this. She gets to the turbo lift. The doors swish open. She enters, tears running down her face.

"Bridge!" She cries.

She put right hand over her mouth and her left over her abdomen. Trying to digest what the doctor just told her.

"Halt turbo lift!" She cries. "FUCK!"

She cries for a moment, pressing both hands in front of her face. She then wipes away the tears realizing she can't walk onto the bridge a wreck. She sniffles and rubs her nose.

"Resume turbo lift!"She says.

The turbo lift doors open. She rushes to her ready room, hiding her face. The doors close behind her. Chakotay stares at the doors wondering what is going on.

 _What the fuck am I going to do? What am I going to tell Chakotay? What will he do_

 _when he finds out? Will he want to keep it? I knew what happened between us was a_

 _mistake! Or was it?_


	3. Chapter 3

**Sorry for taking so long to post! Been a little busy with school! But enough about me, let's get to Captain Janeway and Chakotay!**

"Bee-Boop" The door chimes.

"Computer…"she sniffles, "Who's outside my ready room?" She asks.

"Commander Chakotay!" It replied

She quickly wipes her face free of tears.

"Come in" She says as she looks out the window.

Chakotay walks in, rubbing his hands together nervously.

"So… What did the doctor say?" He asks. She turns to him, with tears filling up in her eyes. "What's wrong?" He asks as he runs over to her, sitting by her side.

She doesn't speak, she just looks straight out the window, gazing at the stars. Tears falling down her cheeks and falling onto the hand fisted under her chin.

"Kathryn, talk to me!" He says as he grabs her hand that is sitting on her lap. She turns to look at him. He wipes the tears off of her face. She grabs his hand, squeezing it tight.

"Chakotay…" she pauses, more tears stream down her face. "The reason I've been feeling so nauseous is because…" She looks down at their hands, trying to find the right words.

"What damn it?" He says impatiently.

She stares into his eyes. "I'm… I'm pregnant." She looks down at their hands entangled together, then looks back at Chakotay.

His mouth open, his eyes wide.

He finally snaps back into reality. "What!" He says, stunned.

"Yes, four months."She says as she wipes her face, then returns her hands back to his.

"So it's…"

"Of course it yours Chakotay."She says quietly.

"Umm." He says, still digesting what she just told him.

Her eyes begin to fill up with tears again, her mind racing with thoughts.

"What the fuck are we going to do? How am I going to be a mother and be a captain of a starship at the same time?" She cries.

"So you're not going to keep it?" He asks, scared of what the answer would be.

"Of course I'm going to keep it. I can't kill this baby; it would feel too much like killing you." She says. She can't stop crying. There are too many thoughts running through her mind at this moment. Chakotay pulls her into his chest. Her tears fall onto his uniform. He feels her breath against his chest. He begins to tear up. Knowing that the woman he loves is about to have his child. He was so happy.

She sits up, pushing herself off his chest. "I'm the captain, how can I make the decisions I make knowing that my child is on board?" She cries. She looks down at her lap trying to think of examples. She looks up at him. "For example, the Year of Hell, do you think I would have continued through Krenim space if I knew the area was in conflict. What if I make the same decision again and end up losing it, or end up losing you? I couldn't bear it." She says with more tears streaming down her cheeks. Chakotay wipes them off. He then holds her face gently with both of his hands.

"Listen to me; you will be the best mother and captain anyone could ever have!" He says. She holds his hands up to her face.

She grabs his hands and holds them in her lap. "Then we should go to the doctor and see what he wants me to do for the next five months, my diet and my appointments. I'm going to need you there with me because this _is_ partially your fault." She says.

She holds her hand to her abdomen, thinking about the baby that's going to be there for the next five months. She grabs Chakotay's hand and places it on her abdomen. He stares at his hand and then looks up and smiles. She looks at him and smiles back.

 **I'll try and post as soon as possible! Please Review!**


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